It is hypothesized that core genes are more essential to a lineage than flexible genes [11, 12], and thus, functional necessity dictates core genome stabilization. However, a growing body of NU7441 datasheet evidences suggests that gene expression level is another important and independent predictor of molecular evolution from prokaryote to eukaryote [13–17]. Therefore, it is possible that Prochlorococcus genome stabilization and streamlining is not only influenced by functional

gene necessity, and further transcriptome analyses are required to explain the genome evolution within this genus. Interestingly, the subspecies Prochlorococcus MED4 has an increased rate of protein evolution and a remarkably reduced genome [7, 9, 18]. These characteristics make it an ideal model organism for examining the evolutionary factors that influence genome evolution. RNA-Seq is a high-throughput sequencing technique that has been widely used for transcriptome profiling [19, 20]. It allows for the identification of operons, untranslated regions (UTRs), novel genes, and non-coding RNAs (ncRNAs) [21–24]. In order to determine the global features of MED4 transcriptome and provide

insight for core genome stabilization at the angle of gene expression, we applied RNA-Seq to ten MED4 samples grown on Pro99 medium and artificial medium for Prochlorococcus (AMP) [25] and collected throughout its LY294002 cell line life cycle (Table 1; Methods). We identified the find more operon structure and UTRs, as well as novel opening reading frames (ORFs) and ncRNAs. By analyzing gene expression data, we infer that gene expression, gene necessity, and mRNA stability influence Prochlorococcus MED4 core genome stabilization. Table 1 Summary of sequenced new ten samples Sample Total pair reads Total mapped rate Total mapped Perfect mapped rate Perfect mapped Gene expression rate All CDS genes Core genome

Flexible genome esl1d 4,615,238 99.5% 4,590,777 97.4% 4,493,396 91.8% 95.1% 85.9% esl3d 6,456,732 97.4% 6,288,857 90.9% 5,867,878 91.5% 94.7% 85.9% esl4d 6,624,400 77.5% 5,133,248 75.8% 5,017,983 92.6% 95.9% 86.9% esl8d 6,449,616 70.4% 4,540,530 70.0% 4,447,655 85.2% 89.0% 78.5% esl10d 6,430,250 67.5% 4,337,847 64.6% 4,155,228 89.5% 93.0% 83.5% amp3d 6,630,721 98.0% 6,499,433 93.6% 6,207,018 95.8% 98.2% 91.5% s6_5h 6,401,265 88.2% 5,646,556 83.8% 5,361,059 88.5% 92.7% 81.1% s6_10h 6,394,044 87.9% 5,617,168 83.4% 5,330,075 89.1% 93.1% 82.1% s24_5h 6,391,818 84.8% 5,417,066 79.4% 5,075,743 92.9% 96.2% 87.0% s24_10h 6,396,571 85.3% 5,453,077 79.2% 5,066,084 92.1% 95.3% 86.